Super-resolution microscopy enables biologists to see the previously invisible by circumventing the classical diffraction limit, and holds promise to broadly transform biomedical research. However, current methods offer only limited resolution and multiplexing power, and tend to require either expensive instrumentation or specialized experimental conditions. They thus have not yet been widely adopted in standard biological labs. We propose a simple and robust super-resolution method based on the programmable autonomous blinking of a nucleic acid fluorescent probe. Unlike existing techniques that rely on the externally controlled stochastic blinking of special fluorophores, our technique utilizes programmable autonomous blinking of a nucleic acid (DNA/RNA) probe with prescribed brightness and blinking frequency. This unprecedented level of molecular control on the blinking behavior of the probe will enable an imaging technique that offers high multiplexing power and resolution. Unlike current super-resolution methods, our programmable blinking technique only requires standard instrumentation and is widely applicable and potentially genetically encodable. Development of this technique will bring the performance, usability, and applicability of super-resolution imaging to a new level, and help transform research practice in diverse biomedical fields.